Working Group 1
Quality Assessment and Reproducibility for Instruments & Images in Light Microscopy
The Consortium for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy (QUAREP-LiMi), formed by the global community of practitioners, researchers, developers, service providers, funders, publishers, policy makers and industry related to the use of light microscopy, is committed to democratizing access to quantitative and reproducible light microscopy and the data generated by it.
Our mission is to provide a comprehensive set of community-agreed guidelines, protocols, automation procedures and other resources aimed at improving quality control, quality assurance, and instrument/method calibration. The stakeholders advocate for the use of the highest level of reproducibility for data generated by light microscopy methods in scientific research and biotechnology applications. In support of achieving its mission, QUAREP-LiMi:
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sanctions Working Groups to form teams that focus on specific technical or outreach topics;
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maintains, disseminates, and teaches best practices, protocols, and software tools; and
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collaborates with providers of reference materials or instrumentation or other tools that enable the easy implementation of best practices at the community level.
We came together in our first online Web meeting on the 28th of April, 2020, with about 50 attendees. By now (24st of April 2024), the network has grown to 620 people from 41 countries worldwide. We have members from academia (research labs, core facilities), national microscopy communities, companies involved in the microscopy business, organizations or institutions related to standardization on a national or international level, and scientific publishers and observers from funding agencies (see the graph below and on the member page for an overview).
Ten working groups (WGs) were established in the 2nd General Meeting on the 9th of July 2020 to bring our common aims quickly forward. Our web page gives an overview of QUAREP-LiMi’s work. In the 3rd General Meeting, WG 11 “Microscopy Publication Standards” and later WGs 12 “Image Visualization and Analysis” and 13 “Phototoxicity” were established. WG 14 “Environment” and 15 “FLIM” are in the process of being established, and WG 8 is restructured to work on “Education, Training and Outreach”.
QUAREP-LiMi operates a NextCloud and an OMERO server, serving as a centralized repository and exchange point for our collective work. These platforms facilitate collaboration and data sharing among our members.
QUAREP-LiMi is absolutely open to new members, and we are looking forward to your contribution. If you are interested in joining our initiative, please fill out our membership form. Use our form for changing your working group (WG) or joining a new WG. For any further questions, please contact us.
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Working Group 2
55th meeting, 13th of October 2025
Meeting date
13/10/2025 @ 5:00 PM (CET/CEST)
Meeting summary
Agenda
- Organizational matters and News
- New name for NBO-Q model
- Update on NBO-Q camera model & glossary
- Discussion about dexel vs pixel text
- Update on theory paper
At the beginning of our meeting, we shared information from the SC meeting: a big NSF grant was approved and process for finding a better suited name for our model was agreed.
Next, we discussed the proposed names for the model to replace NBO-Q and agreed that WG2 endorses the suggestions by WG7: LiMi Model. Our camera part of the model is still in the process of being finished, one more meeting round needs to be organised. Specifically, the definitions and describing texts for pixels (as picture elements) and dexels (as detector elements) need to be finalised. We discussed the suggested definitions and text drafts. In the last part of the meeting, the paper subgroup reported about their progress. The content of the work in progress will be shared on the QUAREP-LiMi cloud, in a folder privat to the paper subgroup.
54th meeting, 8th of September 2025
Meeting date
08/09/2025 @ 5:00 PM (CET/CEST)
Meeting summary
Agenda
- Organizational matters and News
- Update on NBO-Q camera model & glossary
- Updates after the summer break (paper, automation…)
- Decide on next priorities
The meeting welcomed new member Kemp Watson and covered organizational updates from the steering committee, including various project developments and upcoming meetings scheduled for October and November. The working group discussed their focus on detection system performance, including camera models and standardized terminology for microscopy systems, while also addressing the progress of a manuscript related to protocol series. The team reviewed developments of the Nikon toolkit and discussed next steps for their project, including the sequential completion of camera work before moving to other detector types.
53rd meeting, 23rd of June 2025
Meeting date
23/06/2025 @ 5:00 PM (CET/CEST)
Meeting summary
Agenda
- Organizational matters and News
- Report from ELMI 2025
- Update on NBO-Q camera model & glossary
- Report from paper working group
- Next steps
The meeting opened with updates from SC and WG7 meetings, including a report from the NBO-Q camera model and glossary project.
Encouraging news was provided about Nature Publishing Group implementing reproducibility checklists inspired by QUAREP-LiMi’s work. These were mentioned in three recent editorials across major journals. However, concerns were raised as essential information is still missing. A broader conversation on FAIR data sharing followed, highlighting the need to better recognize the cost and effort of data acquisition. QUAREP is encouraged to engage more actively in this direction.
Feedback from ELMI 2025 was very positive—QUAREP-led workshops were well attended and sparked interest among participants, many of whom were new to the initiative. This encouraged us to strengthen our outreach efforts for future international meetings, including next year’s ELMI.
Finally, the paper working group is drafting a publication outlining the foundation of the WG2 protocols. While initial writing has begun, broader input is needed. Future publishing plans for the automation tool and data samples will depend on the setup of OMERO and collaboration with companies.
52nd meeting, 12th of May 2025
Meeting date
12/05/2025 @ 5:00 PM (CET/CEST)
Meeting summary
Agenda
- Organizational matters and News
- QUAREP-LiMi ELMI 2025 workshop contribution
- Report from OMERO subgroup meeting
- Update on NBO-Q camera model & glossary
- Report from paper working group
- Next steps
Summary
We started the meeting with discussing our summer meeting scenario. Due to a public holiday and ELMI 2025, we decided to shift our June meeting to June 23rd. In addition, we decided to skip the meetings in July and August to have time for finishing the camera model and glossary, work on the paper, and have time for vacation. We decided to start again with the regular meeting schedule on September 8th.
This summer meeting organisation was followed by a report from the May steering committee meeting. One great news for WG2 was that the SC endorsed the terminology “dexel” for the detector element versus “pixel” as picture element. Next, we briefly discussed the current status of our ELMI workshop preparation.
This was followed by a report from the QUAREP-LiMi OMERO subgroup meeting. A naming convention was introduced by that subgroup, which everybody needs to follow. We discussed how to implement our spreadsheet terms and how to best automate the upload to OMERO. The WG2 co-chairs will look over tags and naming structure for WG2.
This discussion was followed by an update from the NBO-Q camera model and glossary group. The stakeholder group finished working on the hardware part and will now continue with the settings. The plan is to be finished by the end of this summer.
The WG2 paper working group reported from their first meeting where they summarised paper-related content from our past meeting minutes.
We finalised the meeting with summarising the next steps: finalise the NBO-Q camera model and glossary, work on our paper and collect data for it, support WG7 in their work to calibration metadata, and generalise the automation of our WG2 protocols collection to have it eventually working on all microscopy platforms.
51st meeting, 14th of April 2025
Meeting date
14/04/2025 @ 5:00 PM (CET/CEST)
Meeting summary
After discussing possible scenarios for our WG2 work during summer, we reported from the SC meeting on April 1st. This was followed by a detailed report from the Annual QUAREP-LiMi Meeting that took place April 10th.
The ELMI contribution preparation team reported the submission of three workshop abstracts. Approval was expected to be highly likely (by now all our submitted workshops have been accepted).
The NBO-Q camera glossary team could report that the hardware part is finished! Next, the settings part will be tackled, but is not expected to take that long. The rest of the meeting we spend on collecting topics for WG2 to work on in the future: automation for our WG2 protocols, paper to accompany our WG2 protocol collection, collect data for it, NBO-Q model update for point detectors, amongst others. For each of these topics we need to find people to take the lead and define respective time lines.
50th meeting, 10th of March 2025
Meeting date
10/03/2025 @ 5:00 PM (CET/CEST)
Meeting summary
Agenda points
- Organizational matters and News
- Report from the Annual QUAREP-LiMi meeting
- ELMI 2025 workshop contribution
- Update on NBO-Q camera model & glossary
- Next steps
Summary
This meeting was a bit of a house-keeping meeting. After the report from the March SC meeting we briefly discusses our planned contributions to the Annual QUAREP-LiMi meeting. This was followed by setting up a time line and preparation group for organising our contribution to ELMI2025. Next, we had a quick update on the current status of our NBO-Q camera model and glossary project. We closed the meeting with discussing the next projects we need to tackle. We will first focus on preparing our paper and organising collection of data. We will also have to revisit our long-term goals as next big projects.Working Group 3
Working Group 4
46th meeting, 15th of April 2025
Meeting date
15/04/2025 @ 5:00 PM (CET/CEST)
Meeting summary
WG04 members began the meeting by discussing feedback from the annual meeting. The author list on protocols.io was also addressed, and it was agreed that all co-authors should enter their full institutional address in the affiliation section under the “Organization” sub-tab.
The group also discussed the upload of WG04 data into OMERO and reviewed the adopted naming conventions.
Regarding next steps, members agreed to move forward with improving the first version of the WG04 protocol. The immediate goal is to adapt the protocol for use on confocal spinning disk and widefield microscopy systems.
44th meeting, 18th of February 2025
Meeting date
18/02/2025 @ 5:00 PM (CET/CEST)
Meeting summary
In the latest WG04 meeting, members reviewed the feedback received from a co-chair of another WG on the first version of the protocol. Final adjustments were discussed and agreed upon to refine the document before publication. Additionally, the group addressed authorship matters, ensuring proper acknowledgment of contributions and clarifying the necessary updates to affiliations on protocols.io.
Working Group 5
40th meeting, 13th of June 2024
Meeting date
13/06/2024 @ 3:30 PM (CET/CEST)
Meeting summary
We discussed the ELMI workshop, including how it went and what we could improve. We also covered the process of OMERO uploads and linking them to Airtable for tracking results, as well as the filenaming nomenclature.
Working Group 6
Working Group 7
33rd meeting, 17th of February 2025
Meeting date
17/02/2025 @ 5:00 PM (CET/CEST)
Meeting summary
The meeting covered updates on France BioImaging’s metadata efforts, including OMERO.quay beta testing, buffer server deployment, and authentication improvements. WG10 discussed defining “raw” images and their metadata requirements, emphasizing the need for clarity on file formats. The website report highlighted the need for better organization and visibility of resources, with a proposal to create a landing page and potentially rebrand NBO-Q. Discussions on synonyms and profiles addressed term mapping challenges and possible alias extensions. Additional topics included a McGill student project porting NBO-Q to LinkML and preparations for an ISO discussion at OME2025. The next meeting date requires rescheduling due to Easter.
Working Group 8
Working Group 9
Working Group 10
34th meeting, 10th of December 2024
Meeting date
10/12/2024 @ 4:00 PM (CET/CEST)
Meeting summary
Presentation by Siân Culley (King’s College London): be there!
30th meeting, 12th of March 2024
Meeting date
12/03/2024 @ 4:00 PM (CET/CEST)
Meeting summary
This meeting will be dedicated to a quick review of the RID parameter, a global discussion about the new parameter AS told us about and importantly, the ByLaws document with the need of volunteer candidates for the various positions (SC, EBR, OB).
Working Group 11
40th meeting, 22nd of May 2025
Meeting date
22/05/2025 @ 5:00 PM (CET/CEST)
Meeting summary
1-During the last meeting, you expressed your wish to publish the bare minimal list as a standalone document instead of the comprehensive manuscript we were initially envisioning. The main concerns we have are figuring out the type of journal that accepts this format/content and the fact that there are at least 3 publications providing guidelines/checklists for methods reporting.
2-The second action item was to organize the live document that we created a long time ago in which we determined what was level 1 (required), 2 (depends on the application), 3 (nice to have) to build a logic tree for biologists to generate the appropriate checklist depending on the experiment they did.